NCOR1
nuclear receptor corepressor 1, the group of NCoR/SMRT transcriptional repression complex subunits|Myb/SANT domain containing|Protein phosphatase 1 regulatory subunits
Basic information
Region (hg38): 17:16029065-16218185
Links
Phenotypes
GenCC
Source:
- complex neurodevelopmental disorder (Limited), mode of inheritance: AD
- neurodevelopmental disorder (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (220 variants)
- NCOR1-related_disorder (45 variants)
- not_provided (28 variants)
- NCOR1-related_autism_spectrum_disorder (1 variants)
- Thin_skin (1 variants)
- Hyperlaxity (1 variants)
- Autism_spectrum_disorder (1 variants)
- Developmental_delay (1 variants)
- NCOR1-related_Neurodevelopmental_disorder (1 variants)
- Familial_cancer_of_breast (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NCOR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006311.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 14 | 17 | 31 | |||
| missense | 221 | 12 | 237 | |||
| nonsense | 1 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 1 | 224 | 26 | 20 |
Highest pathogenic variant AF is 0.000026248
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NCOR1 | protein_coding | protein_coding | ENST00000268712 | 45 | 189029 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 3.60e-11 | 125643 | 0 | 105 | 125748 | 0.000418 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.94 | 940 | 1.35e+3 | 0.698 | 0.0000753 | 15835 |
| Missense in Polyphen | 398 | 668.3 | 0.59554 | 7762 | ||
| Synonymous | 0.430 | 470 | 482 | 0.975 | 0.0000274 | 4838 |
| Loss of Function | 9.44 | 15 | 132 | 0.114 | 0.00000780 | 1493 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000358 | 0.000357 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000979 | 0.000979 |
| Finnish | 0.0000466 | 0.0000462 |
| European (Non-Finnish) | 0.000108 | 0.000105 |
| Middle Eastern | 0.000979 | 0.000979 |
| South Asian | 0.00203 | 0.00203 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Mediates transcriptional repression by certain nuclear receptors (PubMed:20812024). Part of a complex which promotes histone deacetylation and the formation of repressive chromatin structures which may impede the access of basal transcription factors. Participates in the transcriptional repressor activity produced by BCL6. Recruited by ZBTB7A to the androgen response elements/ARE on target genes, negatively regulates androgen receptor signaling and androgen-induced cell proliferation (PubMed:20812024). {ECO:0000269|PubMed:14527417, ECO:0000269|PubMed:20812024}.;
- Pathway
- Thyroid hormone signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Androgen receptor signaling pathway;Adipogenesis;Ovarian Infertility Genes;MECP2 and Associated Rett Syndrome;Pathways Affected in Adenoid Cystic Carcinoma;Notch Signaling Pathway;Developmental Biology;Notch;Disease;Signal Transduction;Gene expression (Transcription);mechanism of gene regulation by peroxisome proliferators via ppara;Circadian Clock;Generic Transcription Pathway;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;HDACs deacetylate histones;RNA Polymerase II Transcription;Chromatin modifying enzymes;NR1D1 (REV-ERBA) represses gene expression;Metabolism;Transcriptional regulation of white adipocyte differentiation;Downregulation of SMAD2/3:SMAD4 transcriptional activity;Signaling by NOTCH1;Signaling by NOTCH;AndrogenReceptor;ErbB4 signaling events;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;Chromatin organization;C-MYB transcription factor network;Notch signaling pathway;Nuclear signaling by ERBB4;Signaling by ERBB4;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;Signaling by Receptor Tyrosine Kinases;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Notch-mediated HES/HEY network;Diseases of signal transduction;Validated nuclear estrogen receptor alpha network;NOTCH1 Intracellular Domain Regulates Transcription;Signaling events mediated by HDAC Class I;Regulation of nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.625
Intolerance Scores
- loftool
- 0.467
- rvis_EVS
- -2.14
- rvis_percentile_EVS
- 1.5
Haploinsufficiency Scores
- pHI
- 0.578
- hipred
- Y
- hipred_score
- 0.694
- ghis
- 0.600
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ncor1
- Phenotype
- embryo phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- ncor1
- Affected structure
- neutrophil
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;chromatin organization;transcription by RNA polymerase II;circadian rhythm;regulation of lipid metabolic process;negative regulation of transcription, DNA-templated;negative regulation of JNK cascade;spindle assembly;negative regulation of androgen receptor signaling pathway;regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter;regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter;negative regulation of production of miRNAs involved in gene silencing by miRNA;regulation of fatty acid transport
- Cellular component
- histone deacetylase complex;nuclear chromatin;nucleus;nucleoplasm;cytosol;membrane;Sin3 complex;transcriptional repressor complex;mitotic spindle
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II regulatory region DNA binding;RNA polymerase II activating transcription factor binding;chromatin binding;transcription corepressor activity;protein binding;nuclear hormone receptor binding;histone deacetylase binding;sequence-specific DNA binding;transcription regulatory region DNA binding;thyroid hormone receptor binding